Systematic mapping of chromatin state landscapes during mouse development

Embryogenesis requires epigenetic information that allows each cell to respond appropriately to developmental cues. Histone modifications are core components of a cell’s epigenome, giving rise to chromatin states that modulate genome function. Here, we systematically profile histone modifications in a diverse panel of mouse tissues at 8 developmental stages from 10.5 days post conception until birth, performing a total of 1,128 ChIP-seq assays across 72 distinct tissue-stages. We combine these histone modification profiles into a unified set of chromatin state annotations, and track their activity across developmental time and space. Through integrative analysis we identify dynamic enhancers, reveal key transcriptional regulators, and characterize the role of chromatin-based repression in developmental gene regulation. We also leverage these data to link enhancers to putative target genes, revealing connections between coding and non-coding sequence variation in disease etiology. Our study provides a compendium of resources for biomedical researchers, and achieves the most comprehensive view of embryonic chromatin states to date.

Bing Ren | J. Michael Cherry | Axel Visel | Len A. Pennacchio | Wei Wang | Joseph R. Ecker | J. Seth Strattan | Yin Shen | Diane Trout | Mengchi Wang | Yupeng He | Yunjiang Qiu | Yanxiao Zhang | Jean M. Davidson | Brian A. Williams | Henry Amrhein | Ingrid Plajzer-Frick | Veena Afzal | Diane E. Dickel | Andre Wildberg | Iros Barozzi | Momoe Kato | Bo Ding | Tyler H. Garvin | Catherine S. Pickle | Jennifer A. Akiyama | Sebastian Preissl | J. Cherry | D. Dickel | B. Williams | A. Visel | B. Ren | L. Pennacchio | Wei Wang | Yin Shen | Diane Trout | J. Ecker | D. Gorkin | Henry Amrhein | Yunjiang Qiu | S. Preissl | Yuan Zhao | Yanxiao Zhang | V. Afzal | J. Akiyama | I. Plajzer-Frick | Bo Ding | Hongbo Yang | I. Barozzi | Mengchi Wang | Sora Chee | Brandon J. Mannion | Quan T. Pham | Elizabeth Lee | J. Strattan | J. Ecker | Yupeng He | Ah Young Lee | Bin Li | C. Pickle | Sora Chee | Yoko Fukuda-Yuzawa | David U. Gorkin | Bin Li | Hongbo Yang | Yuan Zhao | Bo Zhang | Anne N. Harrington | Elizabeth A. Lee | Momoe Kato | Yoko Fukuda-Yuzawa | B. Mannion | Andre Wildberg | Joseph R. Ecker | Bo Zhang | Brandon J. Mannion | J. M. Cherry | Len A. Pennacchio | Veena Afzal | David U. Gorkin | Ah Young Lee | J. Seth Strattan | Jean M. Davidson | Jennifer A. Akiyama | Catherine S. Pickle | Tyler H. Garvin | Quan T. Pham | Anne N. Harrington | Elizabeth A. Lee | Brian A. Williams | J. Michael Cherry | Diane E. Dickel | Jean M. Davidson | J. M. Cherry | Brian A. Williams | Andre | Wildberg | Yunjiang | Qiu | Anne N. Harrington | Yoko | Fukuda-Yuzawa

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